Monday, July 27, 2015

Singapore, Day 1

I'm not sure how these reports are going to go, as I did not bring a laptop with me. Also, Blogger is not happy with me logging in from another country. However, I have managed to get a decent sized keyboard on the screen of my iPad Mini, so I can at least type somewhat normally. I will not, however, write about every talk (and my apologies to those speakers who do not get mentioned).

Singapore is as expected — hot and humid; except when one is indoors, and even 24 °C surprisingly feels cold. I have washed most of my shirts once already, to remove the perspiration.

Most people seem to have arrived; indeed, many have already been here for a few days. Myself, I spent Sunday afternoon touring Chinatown, and Little India. The food market at the latter location was unbelievably hot, although the locals did not seem to realize this.

We have now dealt with the first day of talks. No mercy was shown to the uninitiated, and we started with the heavy network stuff right from the start.

This took the form of Dan Gusfeld explaining to us in no uncertain terms that Integer Linear Programming can be used to solve many computational problems that are too hard for Dynamic Programming, using Ancestral Recombination Graphs as his example. When asked about possible connections to actual biology, he patiently explained that this was another matter entirely. Kathi Huber later said the same thing when asked about the loss of biological information resulting from unrooting a rooted network. At the time, she was trying to "bridge the gap" between rooted and unrooted networks, and unrooting them is surprisingly effective way to achieve this.

Luay Nakhleh's talk was my favorite of the day. He is one of the few people in this business who can successfully talk computations to a mathematician and biology to a biologist — most of the rest of us fail at one or the other (or both). Sadly, he pointed out that under the coalescent model any gene tree fits inside any species tree (or network), simply by having the gene coalescences occur after the species root is reached. He also noted that we can't distinguish among reticulation processes on a network, which took away one third of my talk!

We finnished with Jesper Jansson decomposing networks into triangles, which is a neat change from the usual decomposition into triplets, clusters or trees. Along the way, he concluded that we need to keep using a lot of different measures for network to network distances, because none of the current ones are good under all conditions. That is another major difference between trees and networks.